Structural Investigations of HIV-1 Restriction: Roles of Autophagy in TRIM5α and HIV-1 Capsid in Complex with a Novel Inhibitor

Abstract

Human Immunodeficiency Virus type-1, HIV-1, is the primary etiological agent of Acquired Immune Deficiency Syndrome, AIDS, a global pandemic with 1.7 million newly infected persons in 2019 alone. There is no cure to infection, and disease progression can only be prevented by a daily antiretroviral drug regime. Access to treatment, non-compliance, and drug-resistance remains an issue, however the development of new therapeutics can address these concerns. Current therapeutics target viral entry, reverse-transcription, integration, and maturation, all stages of the retroviral lifecycle. The HIV capsid core is crucial to mediating infection during the early stages of infection, is a target of innate immune protein TRIM5α, and a recent category of capsid inhibitor retroviral compounds. TRIM5α, part of the highly conserved TRIM protein family, recognises capsid and restricts HIV-1 infection in Rhesus macaques. The exact mechanism of restriction remains elusive. One hypothesis includes macroautophagy, a cellular bulk-degradation pathway with known implications in host-pathogen interactions. TRIM5α contains a novel α-helical LC3-interacting motif, which mediates the interaction between it and the mATG8 family of proteins. The mATG8 proteins have roles in the core machinery of autophagy and selective xenophagy, a mechanism to target specific substrates such as pathogens, for degradation. The interaction between the LC3-interacting motif in TRIM5α and the mATG8 family shows discriminate specificity, and this interaction may also be found in other TRIM proteins. We performed a structurally informed bioinformatic search to identify putative motifs in other TRIM family proteins and used X-ray crystallographic techniques to investigate methods for determining the molecular mechanisms behind the differences in specificity for TRIM5α and the mATG8 family of proteins. Furthermore, we investigated the mechanism and binding of a novel capsid inhibitor currently in the third-generation of development. We present the X-ray crystallographic structure of HIV-1 capsid protein in complex with the inhibitor 11l and propose a likely mechanism of action. This structure will inform future structure-based compound optimisation.